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A semi-empirical Holstein-Peierls model is used to study the temperature effects on the polaron stability in organic semiconductors at a molecular scale. The approach takes into account both intra- and intermolecular electron-lattice interactions and is aimed at describing charge transport in the system. Particularly, we present a systematic numerical investigation to characterize the influence of both temperature and electric field on the stability as well as mobility of the polaron. It is found that the parameter space for which the polaron is dynamically stable is quite limited and the variations in some of these parameters strongly depend on the temperature. The electric field can play a role in further localizing the charge causing a compression of the lattice distortions associated with the polaron, increasing thereby its stability, up to a field strength of approximately 2.0 mV angstrom(-1). Considering field strengths higher than this critical value, the polaron is annihilated spreading charge through the lattice. Furthermore, we have studied the polaron mobility as a function of the anisotropy of the system, going from a one-dimensional system via a highly anisotropic two-dimensional system to a uniform two-dimensional system. There is a clearly observed mobility edge for the polaron; it exhibits a high mobility in the one-dimensional system but as the coupling in the second dimension is turned on the polaron slows down and becomes immobile in the uniform system. The results provided by this transport mechanism are in good agreement with experimental observations and may provide guidance to improve the charge transport in organic optoelectronic devices.

We report the synthesis and self-assembly of chiral, conformationally flexible C-3-symmetrical trisamides. A strong Cotton effect is observed for the supramolecular polymers in linear alkanes but not in cyclic alkanes. MD simulations suggest 2:1 conformations of the amides within the aggregates in both types of solvents, but a chiral bias in only linear alkanes.

The chemical basis of the blue-black to pink-orange color change on cooking of lobster, due to thermal denaturation of an astaxanthin-protein complex, alpha-crustacyanin, in the lobster carapace, has so far been elusive. Here, we investigate the relaxation of the astaxanthin pigment from its bound enolate form to its neutral hydroxyketone form, as origin of the spectral shift, by analyzing the response of UV-vis spectra of a water-soluble 3-hydroxy-4-oxo-beta-ionone model of astaxanthin to increases in pH, and by performing extensive quantum chemical calculations over a wide range of chemical conditions. The enolization of astaxanthin is consistent with the X-ray diffraction data of beta-crustacyanin (PDB code: 1GKA) whose crystals possess the distinct blue color. We find that enolate formation is possible within the protein environment and associated with a large bathochromic shift, thus offering a cogent explanation for the blue-black color and the response to thermal denaturation and revealing the chemistry of astaxanthin upon complex formation.

We have used time-dependent density functional theory in conjunction with the CAM-B3LYP functional and MWB28/aug-cc-pVDZ basis set to determine non-, near-, and on-resonance Raman spectra for a complex formed by 4-mercaptopyridine (4-Mpy) binding with a Ag-13 cluster via the thiolate Ag-S bond. Geometry optimizations of the Ag-13-4-mpy complex showed an on-top structure directly bound to one Ag atom with the ring of the molecule almost flat with respect to two Ag atoms of the complex. The corresponding B3LYP/MWB28/aug-cc-pVDZ geometry is also an on-top structure directly bound to one Ag atom, but the molecule is directed away from the surface,. The near-resonance Raman calculations were carried out in the infinite lifetime approximation, while the on-resonant Raman excitation profiles were calculated with the complex polarization propagator (CPP) approach, introducing a half width at half-maximum spectral broadening of 0.2 eV. Calculation of the UV-vis spectra of the isolated 4-Mpy and of the Ag-13-4-Mpy complex showed that binding shifts the spectra from deep in the UV to the visible region. Calculation of the near-resonance Raman spectra of the two structures of the complex at 410 (3.025 eV) and 425 nm (2.918 eV) showed a strong enhancement. A very large variation across vibrational modes by a factor of at least 10(3) was found for both the static chemical enhancement and charge-transfer (CT) enhancement mechanisms. ThiS large variation in enhancement factor indicates that B-term Herzberg-Teller scattering is occurring because inactive or very low intensity modes in the static spectra of the molecule are much stronger in both the static and near-resonance spectra of the Complex. From the excitation profile using the CPP method, an overall surface enhancement on the order 10(3) or higher was found for individual modes on excitation into a CT excited state.

In this chapter, it is demonstrated how electronic structure calculations, with focus on density functional theory, can be used to gain insight about on-surface reactions. I first give a brief introduction to how density functional theory can be used to study reactions. The focus is then shifted to two different types of on-surface reactions, highlighting the theoretical work that has been performed to gain detailed atomistic insight into them. First, the state of the art of the theory behind on-surface Ullmann coupling is described. In this reaction, molecular building blocks dehalogenate, which enables them to covalently couple. The most crucial reaction parameters are identified—the diffusion and coupling barriers of surface-supported radicals—and the potential for theory to optimize these is discussed. We then concentrate on the homo-coupling between terminal alkynes, a rudimentarily different process where molecules initially couple before undergoing a dehydrogenation step. The theory of the mechanism behind this coupling strategy is less developed than that of the on-surface Ullmann coupling, where fundamental questions remain to be unraveled. For example, by the subtle change of substrate from Ag to Au, the on-surface alkyne chemistry is completely altered from the homo-coupling to a cyclodehydrogenation reaction for the same molecular building block, of which origin remains unknown. The main objective of the chapter is to give an impression of what kind of information theory can obtain about reaction on surface, as well as to motivate and inspire for future theoretical studies, which will be needed to turn on-surface synthesis into a more predictive discipline.

In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms.

We have computationally studied the effects of temperature on the reaction pathway of an electrocyclic ring-closure reaction on the Au(111) surface, particularly focusing on thermodynamic aspects of the reaction. The electrocyclic ring closure is accompanied by a series of dehydrogenation steps, and while it is found that temperature, in terms of vibrational entropy and enthalpy, has a reducing effect on most energy barriers, it does not alter the qualitative appreciation of the reaction kinetics. However, it is found that the way the abstracted hydrogen atoms are treated is crucial for the thermodynamics of the reaction. The overall reaction is highly endothermic but becomes thermodynamically favorable due to the entropy gain of the hydrogen byproducts, which desorb associatively from the surface as H2. The study provides new outlooks for the theoretical treatment of reactions related to on-surface synthesis, anticipated to be instructive for future studies.

The fabrication of graphene nanoribbons (GNRs) requires a high degree of precision due to the sensitivity of the electronic structure on the edge shape. Using Br-substituted molecular precursors, this atomic precision can be achieved in a thermally induced two-step reaction following Br dissociation on a Au(111) surface. Using DFT, we find evidence that the Br atoms are bound to the intermediate polyanthrylene chains. We employ temperature-programmed desorption to demonstrate the associative desorption of HBr and molecular hydrogen during the final cyclodehydrogenation step of the reaction. Both processes are found to have similar activation barriers. Furthermore, we are able to remove Br atoms from the polyanthrylene chains by providing molecular hydrogen. The subsequent formation of GNR via a cyclodehydrogenation demonstrates that Br does not influence this part of the overall reaction.

On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

A computational protocol for magneto-chiral dichroism and magneto-chiral birefringence dispersion is presented within the framework of damped response theory, also known as complex polarization propagator theory, at the level of time-dependent Hartree-Fock and time-dependent density functional theory. Magneto-chiral dichroism and magneto-chiral birefringence spectra in the (resonant) frequency region below the first ionization threshold of R-methyloxirane and L-alanine are presented and compared with the corresponding results obtained for both the electronic circular dichroism and the magnetic circular dichroism. The additional information content yielded by the magneto-chiral phenomena, as well as their potential experimental detectability for the selected species, is discussed.

Long-range non-covalent interactions play a key role in the chemistry of natural polyphenols. We have previously proposed a description of supramolecular polyphenol complexes by the B3P86 density functional coupled with some corrections for dispersion. We couple here the B3P86 functional with the D3 correction for dispersion, assessing systematically the accuracy of the new B3P86-D3 model using for that the well-known S66, HB23, NCCE31, and S12L datasets for non-covalent interactions. Furthermore, the association energies of these complexes were carefully compared to those obtained by other dispersion-corrected functionals, such as B(3) LYP-D3, BP86-D3 or B3P86-NL. Finally, this set of models were also applied to a database composed of seven non-covalent polyphenol complexes of the most interest.

A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment.

This study presents the influence of various substituents on the photophysical features of heteroleptic copper(I) complexes bearing both N-heterocyclic carbene (NHC) and dipyridylamine (dpa = dipyridylamine skeleton corresponding to ligand L1) ligands. The luminescent properties have been compared to our recently reported archetypal blue emitting [Cu(IPr)(dpa)][PF6] complex. The choice of the substituents on both ligands has been guided to explore the effect of the electron donor/acceptor and "push-pull" on the emission wavelengths and photoluminescence quantum yields. A selection of the best candidates in terms of their photophysical features were applied for developing the first blue light emitting electrochemical cells (LECs) based on copper(I) complexes. The device analysis suggests that the main concern is the moderate redox stability of the complexes under high applied driving currents, leading to devices with moderate stabilities pointing to a proof-of-concept for further development. Nevertheless, under low applied driving currents the blue emission is stable, showing performance levels competitive to those reported for blue LECs baged on iridium(III) complexes. Overall, this work provides valuable guidelines to tackle the design of enhanced NHC copper complexes for lighting applications in the near future.

The Rayleigh light scattering properties of (H2SO4)(a)(NH3)(b) and (H2SO4)(a)((CH3)(2)NH)(b) atmospheric molecular clusters have been investigated using a response theory approach. Using density functional theory the molecular structures and stepwise formation free energies of clusters with a and b up to 4 have been re-investigated. The Rayleigh scattering intensities are calculated from the dipole polarizability tensor a using the CAM-B3LYP functional by applying linear response methods. The intrinsic scattering properties of (H2SO4)(a)(NH3)(b) and (H2SO4)(a)((CH3)(2)NH)(b) indicate that amine containing clusters scatter light significantly more efficiently then their ammonia containing counterparts. Using the Atmospheric Cluster Dynamics Code (ACDC) the steady state cluster concentrations are estimated and the effective scattering is calculated. The effective scattering is shown to be highly dependent on the estimated concentrations and indicates that there exist competitive pathways, such as nucleation and coagulation, which influence the cluster distributions. The frequency dependence of the scattering is found to depend on the cluster composition and show increased responses when clusters contain more bases than acid molecules. Based on structures obtained using semi-empirical molecular dynamics simulations the Rayleigh scattering properties of clusters with up to 20 acid-base pairs are evaluated. This study represents the first step towards gaining a fundamental understanding of the scattering properties of small atmospheric clusters in the ambient atmosphere.

Molecular response to electromagnetic fields - static or optical - within a framework of perturbation theory diverges close to resonance with molecular transitionen energies, and need work-around solutions for real-valued response functions. This licentiate thesis deals with nonlinear response, with focus being on cubic polarizaibilities, and outlines the underlying mathematics for exact-state and approximatestate, complex-valued response functions applicable to quantum chemical computation. Such a complex-valued response theory is commonly known as dampedresponse theory, for which the response functions consists of a real and an imaginary component, each of them representing various spectroscopies in nature. In addition to the mathematics, the formulas have been implemented in the quantum chemical package DALTON, and several tests determining the integrity of the implementation has been conducted.

The fourth and final major part of the thesis is concerned with applied nonlinear response theory, including not only cubic response functions, but also quadratic and linear response functions, some of which are of the more exotic character. Three spectroscopies have been investigated for small and medium-sized organic molecules and the neon atom: two-photon absorption (TPA), Jones birefringence (JB), and magnetic circular dichroism (MCD).

The TPA part is a simple demonstration of capability of the damped cubic response code, for which neon is the example system. Perfect agreement is shown for the Ehrenfest approach and an independent implementation based on the quasienergy formalism.

JB is an optical eect in which induced refractive anisotropy, by means of external electric and magnetic static elds, results in ellipticity of linearly polarized light beams. This part mainly discuss implications from a paper which the current author took part in. The paper ultimately attempts to indentify the general observable strength of the effect, and coincidentaly pin-point some particular system suitable for experiments. Among other finds, JB is found to be correlated to the electric dipole moment, and for monosubstituted benzenes, the para-Hammett constant.

Finally, MCD is discussed based on three papers in which the present author is included. The elegant MCD solution to broad absorption peaks, for which it is desired to distinguish individual states, is demonstrated on adenine and three additional purine derivatives. A drawn out debate regarding relative stability of certain low-lying states could be settled by this method. Furthermore, appropriate description of solvation environment in conjunction with the exchange-correlation functionals B3LYP and CAM-B3LYP is investigated on purine and pyrimidine derivatives. CAM-B3LYP is found to be superior in terms of general prole shapes, while results regarding solvation model are rather inconclusive, although the results suggests some level of solvation model is appropriate, such as a polarizable continuum model or explicit solvation molecules.

Coriani, Sonia

Abstract [en]

The magnetic circular dichroism spectrum of the C-60 fullerene has been determined with the use of Kohn-Sham density functional theory in conjunction with the CAM-B3LYP exchange-correlation functional. The experimental spectrum of Gasyna etal. [Chem. Phys. Lett. 183, 283 (1991)] covering the wavelength region above 200 nm is explained by the signal responses from the three lowest singlet states of T-1u symmetry.

Rikken, Geert L J A

Abstract [en]

We report on the results of a systematic ab initio study of the Jones birefringence of noble gases, of furan homologues, and of monosubstituted benzenes, in the gas phase, with the aim of analyzing the behavior and the trends within a list of systems of varying size and complexity, and of identifying candidates for a combined experimental/theoretical study of the effect. We resort here to analytic linear and nonlinear response functions in the framework of time-dependent density functional theory. A correlation is made between the observable (the Jones constant) and the atomic radius for noble gases, or the permanent electric dipole and a structure/chemical reactivity descriptor as the para Hammett constant for substituted benzenes.

Abstract [en]

The relative position of L-a and L-b pi pi* electronic states in purine nucleobases is a much debated topic, since it can strongly affect our understanding of their photoexcited dynamics. To assess this point, we calculated the absorption and magnetic circular dichroism (MCD) spectra of adenine, guanine, and their nucleosides in gas-phase and aqueous solution,. exploiting recent developments in MCD computational technology within time-dependent density functional theory. MCD spectroscopy allows us to resolve the intense S-0 -greater than L-a transition from the weak S-0 -greater than L-b transition. The spectra obtained in water solution, by using B3LYP and CAM-B3LYP functionals and describing solvent effect by cluster models and by the polarizable continuum model (PCM), are in very good agreement with the experimental counterparts, thus providing direct and unambiguous evidence that the energy ordering predicted by TD-DFT, L-a less than L-b, is the correct one.

Abstract [en]

We present a computational study of the Magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil,thymine, and cytosine, Using the B3LYP and CAM-B3LYP functionals. Solvent effects, are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In, general; the computed spectra are found to be in good agreement with the experimental ones, aprt from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine base are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to,that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific,but they do not in general alter the qualitative shape of the spectra. The bands are dominated the-bright pi -greater than pi* transitions; and our calculations in solution nicely reproduce theft energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n -greater than pi* excitations, but they are too weak to be observed in the. experiment.

We present a computational study of the Magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil,thymine, and cytosine, Using the B3LYP and CAM-B3LYP functionals. Solvent effects, are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In, general; the computed spectra are found to be in good agreement with the experimental ones, aprt from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine base are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to,that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific,but they do not in general alter the qualitative shape of the spectra. The bands are dominated the-bright pi -greater than pi* transitions; and our calculations in solution nicely reproduce theft energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n -greater than pi* excitations, but they are too weak to be observed in the. experiment.

A complex polarization propagator approach has been developed to third order and implemented in density functional theory (DFT), allowing for the direct calculation of nonlinear molecular properties in the X-ray wavelength regime without explicitly addressing the excited-state manifold. We demonstrate the utility of this propagator method for the modeling of coherent near-edge X-ray two-photon absorption using, as an example, DFT as the underlying electronic structure model. Results are compared with the corresponding near edge X-ray absorption fine structure spectra, illuminating the differences in the role of symmetry, localization, and correlation between the two spectroscopies. The ramifications of this new technique for nonlinear X-ray research are briefly discussed.

The rst part of the thesis is concerned with two protein-bound chromophores that, depending on the chemical conditions, can exist in a number of dierent ketonic and enolic forms. The rst chromophore is astaxanthin, which occurs in the protein complex responsible for the deep-blue color of lobster carapace. By investigating how dierent forms of astaxanthin absorb UV-vis radiation of dierent wavelengths, a model is presented that explains the origin of the dramatic color change from deep-blue to red upon cooking of live lobsters.

The second chromophore is the oxyluciferin light emitter of fireflies, which is formed in the catalytic center of the enzyme firefly luciferase. To date, there is no consensus regarding which of the possible ketonic and enolic forms is the key contributor to the light emission. In the thesis, the intrinsic tendency of oxyluciferin to prefer one particular form over other possible forms is established through calculation of keto-enol and acid-base excited-state equilibrium constants in aqueous solution.

The second part of the thesis is concerned with two families of biological photoreceptors: the blue-light-absorbing LOV-domain proteins and the red-light-absorbing phytochromes. Based on the ambient light environment, these proteins regulate physiological and developmental processes by switching between inactive and active conformations. In both families, the conversion of the inactive into the active conformation is triggered by a chemical reaction of the respective chromophore.

The LOV-domain proteins bind a LOV-domain proteins bidn in flavin chromophore and regulate processes such as chloroplast relocation and phototropism in plants. An important step in the activation of these photoreceptors is a singlet-triplet transition between two electronically excited states of the flavin chromophore. In the thesis, this transition is used as a prototype example for illustrating, for the rst time, the ability of rst-principles methods to calculate rate constants of inter-excited state phosphorescence events.

Phytochromes, in turn, bind bilin chromophores and are active in the regulation of processes like seed germination and flowering time in plants. Following two systematic studies identifying the best way to model the UV-vis absorption and fluorescence spectra of these photoreceptors, it is demonstrated that steric interactions between the chromophore and the apoprotein play a decisive role for how phytochromes are activated by light.

Abstract [en]

The chemical basis of the blue-black to pink-orange color change on cooking of lobster, due to thermal denaturation of an astaxanthin-protein complex, alpha-crustacyanin, in the lobster carapace, has so far been elusive. Here, we investigate the relaxation of the astaxanthin pigment from its bound enolate form to its neutral hydroxyketone form, as origin of the spectral shift, by analyzing the response of UV-vis spectra of a water-soluble 3-hydroxy-4-oxo-beta-ionone model of astaxanthin to increases in pH, and by performing extensive quantum chemical calculations over a wide range of chemical conditions. The enolization of astaxanthin is consistent with the X-ray diffraction data of beta-crustacyanin (PDB code: 1GKA) whose crystals possess the distinct blue color. We find that enolate formation is possible within the protein environment and associated with a large bathochromic shift, thus offering a cogent explanation for the blue-black color and the response to thermal denaturation and revealing the chemistry of astaxanthin upon complex formation.

Abstract [en]

Although recent years have seen much progress in the elucidation of the mechanisms underlying the bioluminescence of fireflies, there is to date no consensus on the precise contributions to the light emission from the different possible forms of the chemiexcited oxyluciferin (OxyLH(2)) cofactor. Here, this problem is investigated by the calculation of excited-state equilibrium constants in aqueous solution for keto-enol and acid-base reactions connecting six neutral, monoanionic and dianionic forms of OxyLH(2). Particularly, rather than relying on the standard Forster equation and the associated assumption that entropic effects are negligible, these equilibrium constants are for the first time calculated in terms of excited-state free energies of a Born-Haber cycle. Performing quantum chemical calculations with density functional theory methods and using a hybrid cluster-continuum approach to describe solvent effects, a suitable protocol for the modeling is first defined from benchmark calculations on phenol. Applying this protocol to the various OxyLH(2) species and verifying that available experimental data (absorption shifts and ground-state equilibrium constants) are accurately reproduced, it is then found that the phenolate-keto-OxyLH(-) monoanion is intrinsically the preferred form of OxyLH(2) in the excited state, which suggests a potential key role for this species in the bioluminescence of fireflies.

Abstract [en]

Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states, can be supplemented by the ability to also describe inter-excited state phosphorescence. Specifically, performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL*) singlet state of lumiflavin to the 3(πHπL*), 3(nN2πL*) and 3(πH–1πL*) triplet states, and subsequently compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically two to five orders of magnitude smaller than the nonradiative ones.

Abstract [en]

Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.

Abstract [en]

Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

Durbeej, Bo

Abstract [en]

Phytochromes constitute a superfamily of photoreceptor proteins that exist in two forms that absorb red (Pr) and far-red (Pfr) light. The conversion of Pr into Pfr (the biologically active form) is triggered by a Z → E photoisomerization of the bilin chromophore at the C15-C16 bond of the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on a highresolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions prevent photoisomerization at any other site than the C15-C16 bond. The tendency of phytochromes to always isomerize at this very bond would thus be explained by steric effects.

Phytochromes constitute a superfamily of photoreceptor proteins that exist in two forms that absorb red (Pr) and far-red (Pfr) light. The conversion of Pr into Pfr (the biologically active form) is triggered by a Z → E photoisomerization of the bilin chromophore at the C15-C16 bond of the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on a highresolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions prevent photoisomerization at any other site than the C15-C16 bond. The tendency of phytochromes to always isomerize at this very bond would thus be explained by steric effects.

Phytochromes constitute a superfamily of photoreceptor proteins existing in two forms that absorb red (Pr) and far-red (Pfr) light. Although it is well-known that the conversion of Pr into Pfr (the biologically active form) is triggered by a ZE photoisomerization of the linear tetrapyrrole chromophore, direct evidence is scarce as to why this reaction always occurs at the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics calculations based on a high-resolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions render photoisomerizations at the AB and BC bridges much less probable than photoisomerization at the CD bridge.

Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states, can be supplemented by the ability to also describe inter-excited state phosphorescence. Specifically, performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL*) singlet state of lumiflavin to the 3(πHπL*), 3(nN2πL*) and 3(πH–1πL*) triplet states, and subsequently compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically two to five orders of magnitude smaller than the nonradiative ones.

The impurity effects on the dynamics of polarons in armchair graphene nanoribbons are numerically investigated in the scope of a two-dimensional tight-binding approach with lattice relaxation. The results show that the presence of an impurity changes significantly the net charge distribution associated to the polaron structure. Moreover, the interplay between external electric field and the local impurities plays the role of drastically modifying the polaron dynamics. Interestingly, nanoribbons containing mobile polarons are noted to take place even when considering high impurity levels, which is associated with the highly conductive character of the graphene nanoribbons. This investigation may enlighten the understanding of the charge transport mechanism in carbon-based nanomaterials. (C) 2015 Elsevier Ltd. All rights reserved.

Quercetin is a prototypical antioxidant and prominent member of flavonoids, a large group of natural polyphenols. The oxidation of quercetin may lead to its dimerization, which is a paradigm of the more general polyphenol oligomerization. There exist two opposing mechanisms to describe the dimerization process, namely radical-coupling or Diels-Alder reactions. This work presents a comprehensive rationalization of this dimerization process, acquired from density functional theory (DFT) calculations. It is found that the two-step radical-coupling pathway is thermodynamically and kinetically preferred over the Diels-Alder reaction. This is in agreement with the experimental results showing the formation of only one isomer, whereas the Diels-Alder mechanism would yield two isomers. The evolution in bonding, occurring during these two processes, is investigated using the atoms in molecules (AIM) and electron localization function (ELF) topological approaches. It is shown that some electron density is accumulated between the fragments in the transition state of the radical-coupling reaction, but not in the transition state of the Diels-Alder process.

In order to reach a fundamental understanding of interactions between electromagnetic radiation and molecular materials, experimental measurements need to be supplemented with theoretical models and simulations. With the use of this combination, it is possible to characterize materials in terms of, e.g., chemical composition and molecular structure, as well as achieve time-resolution in studies of chemical reactions. This doctoral thesis focuses on the development and evaluation of theoretical methods with which, amongst others, X-ray absorption and X-ray emission spectroscopies can be interpreted and predicted. In X-ray absorption spectroscopy the photon energy is tuned such that core electrons are targeted and excited to either bound or continuum states, and X-ray emission spectroscopy measures the subsequent decay from such an excited state. These core excitations/de-excitations exhibit strong relaxation effects, making theoretical considerations of the processes particularly challenging. While the removal of a valence electron leaves the remaining electrons relatively unaffected, removing core electrons has a substantial effect on the other electrons due to the significant change in the screening of the nucleus. Additionally, the core-excited states are embedded in a manifold of valence-excited states that needs to be considered by some computationally feasible method. In this thesis, a damped formalism of linear response theory, which is a perturbative manner of considering the interactions of (weak) external or internal fields with molecular systems, has been utilized to investigate mainly the X-ray absorption spectra of small- to medium-sized molecular systems.

Amongst the standard quantum chemical methods available, coupled cluster is perhaps the most accurate, with a well-defined, hierarchical manner of approaching the correct electronic wave function. Combined with response theory, it provides a reliable theoretical method in which relaxation effects are addressed by means of an accurate treatment of electron correlation. The first part of this thesis deals with the development and evaluation of such an approach, and it is shown that the relaxation effects can be addressed by the inclusion of double excitations in the coupled cluster manifold. However, these calculations are computationally very demanding, and in order to treat larger systems the performance of the coupled cluster approach has been compared to that of the less demanding method of time-density dependent functional theory (TDDFT). Both methods have been used to investigate the X-ray absorption spectrum of water, which has been extensively debated in the scientific community following a relatively recent hypothesis concerning the underlying structure of liquid water. Water exhibits a great number of anomalous properties that stand out from those of most compounds, and the importance of reaching a fundamental understanding of this substance cannot be overstated. It has been demonstrated that TDDFT yields excellent results for liquid water, opening up possibilities of investigating the correlation between spectral features and local structures.

Furthermore, recent developments in damped linear response TDDFT in the four-component relativistic regime have enabled the inclusion of spin-orbit coupling in damped linear response calculations, making black-box calculations of absorption spectra in a relativistic setting practical. With this approach, it is possible to address the spin-orbit splitting in L2,3-edge X-ray absorption spectra, and the performance of such a method has been demonstrated for a set of small molecules. Excellent agreement with experiment is obtained in terms of relative features, but an anomalous error in absolute energy has been observed for silane derivatives featuring fluorine-substitutions. This is likely a result of the strong influence of the very electronegative fluorine atoms on the electron density of the core-excited atom.

Finally, the treatment of non-resonant X-ray emission spectroscopy using damped linear response theory is discussed. The expansion needed for the development of a simple method by which this spectroscopy can be treated using damped linear response theory at the TDDFT level of theory has been identified, and proof of principle calculations at the time-dependent Hartree-Fock level of theory are presented.

Abstract [en]

Based on an asymmetric Lanczos-chain subspace algorithm, damped coupled cluster linear response functions have been implemented for the hierarchy of coupled cluster (CC) models including CC with single excitations (CCS), CC2, CC with single and double excitations (CCSD), and CCSD with noniterative triple corrected excitation energies CCSDR(3). This work is a first step toward the extension of these theoretical electronic structure methods of well-established high accuracy in UV-vis absorption spectroscopies to applications concerned with x-ray radiation. From the imaginary part of the linear response function, the near K-edge x-ray absorption spectra of neon, water, and carbon monoxide are determined and compared with experiment. Results at the CCSD level show relative peak intensities in good agreement with experiment with discrepancies in transition energies due to incomplete treatment of electronic relaxation and correlation that amount to 1-2 eV. With inclusion of triple excitations, errors in energetics are less than 0.9 eV and thereby capturing 90%, 95%, and 98% of the relaxation-correlation energies for C, O, and Ne, respectively.

Abstract [en]

We present an implementation of the damped coupled-cluster linear response function based on an asymmetric Lanczos chain algorithm for the hierarchy of coupled-cluster approximations CCS (coupled-cluster singles), CC2 (coupled. cluster singles and approximate doubles), and CCSD (coupled-cluster singles and doubles). Triple corrections to the excitation energies can be included via the CCSDR(3) (coupled-cluster singles and doubles with noniterative-triples-corrected excitation energies) approximation. The performance and some of the potentialities of the approach are investigated in calculations of the visible/ultraviolet absorption spectrum and the dispersion of the real polarizability in near-resonant regions of pyrimidine, the near-edge absorption fine structure (NEXAFS) of ammonia, and the direct determination of the C-6 dipole-dipole dispersion coefficient of the benzene dimer.

Abstract [en]

Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger pi-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to pi*-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate pi*-peak separations due to spectral compressions, a characteristic which is inherent to this method.

Abstract [en]

A computational benchmark study on X-ray absorption spectra of water has been performed by means of transition-potential density functional theory (TP-DFT), damped time-dependent density functional theory (TDDFT), and damped coupled cluster (CC) linear response theory. For liquid water, using TDDFT with a tailored CAM-B3LYP functional and a polarizable embedding, we find that an embedding with over 2000 water molecules is required to fully converge spectral features for individual molecules, but a substantially smaller embedding can be used within averaging schemes. TP-DFT and TDDFT calculations on 100 MD structures demonstrate that TDDFT produces a spectrum with spectral features in good agreement with experiment, while it is more difficult to fully resolve the spectral features in the TP-DFT spectrum. Similar trends were also observed for calculations of bulk ice. In order to further establish the performance of these methods, small water clusters have been considered also at the CC2 and CCSD levels of theory. Issues regarding the basis set requirements for spectrum simulations of liquid water and the determination of gas-phase ionization potentials are also discussed.

Abstract [en]

The influences of group 12 (Zn, Cd, Hg) metal-substitution on the valence spectra and phosphorescence parameters of porphyrins (P) have been investigated in a relativistic setting. In order to obtain valence spectra, this study reports the first application of the damped linear response function, or complex polarization propagator, in the four-component density functional theory framework [as formulated in J. Chem. Phys. 133, 064105 (2010)]. It is shown that the steep increase in the density of states as due to the inclusion of spin-orbit coupling yields only minor changes in overall computational costs involved with the solution of the set of linear response equations. Comparing single-frequency to multi-frequency spectral calculations, it is noted that the number of iterations in the iterative linear equation solver per frequency grid-point decreases monotonously from 30 to 0.74 as the number of frequency points goes from one to 19. The main heavy-atom effect on the UV/vis-absorption spectra is indirect and attributed to the change of point group symmetry due to metal-substitution, and it is noted that substitutions using heavier atoms yield small red-shifts of the intense Soret-band. Concerning phosphorescence parameters, the adoption of a four-component relativistic setting enables the calculation of such properties at a linear order of response theory, and any higher-order response functions does not need to be considered. For the substituted porphyrins, electronic coupling between the lowest triplet states is strong and results in theoretical estimates of lifetimes that are sensitive to the wave function and electron density parametrization. With this in mind, we report our best estimates of the phosphorescence lifetimes to be 460, 13.8, 11.2, and 0.00155 s for H2P, ZnP, CdP, and HgP, respectively, with the corresponding transition energies being equal to 1.46, 1.50, 1.38, and 0.89 eV.

Abstract [en]

X-ray absorption spectra of carbon, silicon, germanium, and sulfur compounds have been investigated by means of damped four-component density functional response theory. It is demonstrated that a reliable description of relativistic effects is obtained at both K- and L-edges. Notably, an excellent agreement with experimental results is obtained for L2,3-spectra—with spin-orbit effects well accounted for—also in cases when the experimental intensity ratio deviate from the statistical one of 1:2. The theoretical results are consistent with calculations using standard response theory as well as recently reported real-time propagation methods in time-dependent density functional theory, and the virtues of different approaches are discussed. As compared to silane and silicon tetrachloride, an anomalous error in the absolute energy is reported for the L2,3-spectrum of silicon tetrafluoride, amounting to an additional spectral shift of ~ 1 eV. This anomaly is observed also for other exchange-correlation functionals, but it is seen neither at other silicon edges nor at the carbon K-edge of fluorine derivatives of ethene. Considering the series of molecules SiH4−XFX with X = 1, 2, 3, 4, a gradual divergence from interpolated experimental ionization potentials is observed at the level of Kohn–Sham density functional theory (DFT), and to a smaller extent with use of Hartree–Fock. This anomalous error is thus attributed partly to difficulties in correctly emulating the electronic structure effects imposed by the very electronegative fluorines, and partly due to inconsistencies in the spurious electron self-repulsion in DFT. Substitution with one, or possibly two, fluorine atoms is estimated to yield small enough errors to allow for reliable interpretations and predictions of L2,3-spectra of more complex and extended silicon-based systems.

X-ray absorption spectra of carbon, silicon, germanium, and sulfur compounds have been investigated by means of damped four-component density functional response theory. It is demonstrated that a reliable description of relativistic effects is obtained at both K- and L-edges. Notably, an excellent agreement with experimental results is obtained for L2,3-spectra—with spin-orbit effects well accounted for—also in cases when the experimental intensity ratio deviate from the statistical one of 1:2. The theoretical results are consistent with calculations using standard response theory as well as recently reported real-time propagation methods in time-dependent density functional theory, and the virtues of different approaches are discussed. As compared to silane and silicon tetrachloride, an anomalous error in the absolute energy is reported for the L2,3-spectrum of silicon tetrafluoride, amounting to an additional spectral shift of ~ 1 eV. This anomaly is observed also for other exchange-correlation functionals, but it is seen neither at other silicon edges nor at the carbon K-edge of fluorine derivatives of ethene. Considering the series of molecules SiH4−XFX with X = 1, 2, 3, 4, a gradual divergence from interpolated experimental ionization potentials is observed at the level of Kohn–Sham density functional theory (DFT), and to a smaller extent with use of Hartree–Fock. This anomalous error is thus attributed partly to difficulties in correctly emulating the electronic structure effects imposed by the very electronegative fluorines, and partly due to inconsistencies in the spurious electron self-repulsion in DFT. Substitution with one, or possibly two, fluorine atoms is estimated to yield small enough errors to allow for reliable interpretations and predictions of L2,3-spectra of more complex and extended silicon-based systems.

Here we present an overview of recent developments of X-ray and electron spectroscopy to probe water at different temperatures. Photon-induced ionization followed by detection of electrons from either the 0 is level or the valence band is the basis of photoelectron spectroscopy. Excitation between the 0 is and the unoccupied states or occupied states is utilized in X-ray absorption and X-ray emission spectroscopies. These techniques probe the electronic structure of the liquid phase and show sensitivity to the local hydrogen-bonding structure. Both experimental aspects related to the measurements and theoretical simulations to assist in the interpretation are discussed in detail. Different model systems are presented such as the different bulk phases of ice and various adsorbed monolayer structures on metal surfaces.

The influences of group 12 (Zn, Cd, Hg) metal-substitution on the valence spectra and phosphorescence parameters of porphyrins (P) have been investigated in a relativistic setting. In order to obtain valence spectra, this study reports the first application of the damped linear response function, or complex polarization propagator, in the four-component density functional theory framework [as formulated in J. Chem. Phys. 133, 064105 (2010)]. It is shown that the steep increase in the density of states as due to the inclusion of spin-orbit coupling yields only minor changes in overall computational costs involved with the solution of the set of linear response equations. Comparing single-frequency to multi-frequency spectral calculations, it is noted that the number of iterations in the iterative linear equation solver per frequency grid-point decreases monotonously from 30 to 0.74 as the number of frequency points goes from one to 19. The main heavy-atom effect on the UV/vis-absorption spectra is indirect and attributed to the change of point group symmetry due to metal-substitution, and it is noted that substitutions using heavier atoms yield small red-shifts of the intense Soret-band. Concerning phosphorescence parameters, the adoption of a four-component relativistic setting enables the calculation of such properties at a linear order of response theory, and any higher-order response functions does not need to be considered. For the substituted porphyrins, electronic coupling between the lowest triplet states is strong and results in theoretical estimates of lifetimes that are sensitive to the wave function and electron density parametrization. With this in mind, we report our best estimates of the phosphorescence lifetimes to be 460, 13.8, 11.2, and 0.00155 s for H2P, ZnP, CdP, and HgP, respectively, with the corresponding transition energies being equal to 1.46, 1.50, 1.38, and 0.89 eV.

The epitaxial growth of graphene on catalytically active metallic surfaces via chemical vapor deposition (CVD) is known to be one of the most reliable routes toward high-quality large-area graphene. This CVD-grown graphene is generally coupled to its metallic support resulting in a modification of its intrinsic properties. Growth on oxides is a promising alternative that might lead to a decoupled graphene layer. Here, we compare graphene on a pure metallic to graphene on an oxidized copper surface in both cases grown by a single step CVD process under similar conditions. Remarkably, the growth on copper oxide, a high-k dielectric material, preserves the intrinsic properties of graphene; it is not doped and a linear dispersion is observed close to the Fermi energy. Density functional theory calculations give additional insight into the reaction processes and help explaining the catalytic activity of the copper oxide surface.

We present a formulation of molecular response theory for the description of a quantum mechanical molecular system in the presence of a weak, monochromatic, linearly polarized electromagnetic field without introducing truncated multipolar expansions. The presentation focuses on a description of linear absorption by adopting the energy-loss approach in combination with the complex polarization propagator formulation of response theory. Going beyond the electric-dipole approximation is essential whenever studying electric-dipole-forbidden transitions, and in general, non-dipolar effects become increasingly important when addressing spectroscopies involving higher-energy photons. These two aspects are examined by our study of the near K-edge X-ray absorption fine structure of the alkaline earth metals (Mg, Ca, Sr, Ba, and Ra) as well as the trans-polyenes. In following the series of alkaline earth metals, the sizes of non-dipolar effects are probed with respect to increasing photon energies and a detailed assessment of results is made in terms of studying the pertinent transition electron densities and in particular their spatial extension in comparison with the photon wavelength. Along the series of trans-polyenes, the sizes of non-dipolar effects are probed for X-ray spectroscopies on organic molecules with respect to the spatial extension of the chromophore.

Based on the recently developed implementation of the full semi-classical field-matter interaction operator, we present a numerically accurate yet efficient scheme to perform rotational averaging of linear absorption spectra beyond the electric-dipole approximation. This allows for a gauge-origin independent determination of UV/vis and X-ray absorption spectra for randomly oriented systems such as multilayers, liquids, and gas phase samples. The approach is illustrated by the determination of spectral intensities of electric-dipole allowed pi -amp;gt; pi* transitions and electric-dipole forbidden n -amp;gt;pi* transitions in the UV-vis region of the spectrum as well as electric-dipole forbidden 1s. 3d transitions in the X-ray region of the spectrum. The employed Lebedev quadrature scheme shows very fast convergence with respect to the number of symmetry-independent quadrature points-in all considered cases, the oscillator strengths for the randomly oriented systems are fully converged with use of only seven quadrature points. [GRAPHICS]

Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar–Xe, Kr–Xe and Xe–Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal–organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems.

CONSPECTUS: The covalent linking of acetylene compounds is an important synthetic tool to control carbon carbon bond formation and has been extensively studied for more than a century. Notably, Glaser coupling and subsequently developed refined procedures present an important route for the fabrication of distinct carbon-based scaffolds incorporating units with both sp(2)- and sp-hybridizations, such as carbyne chains, or two-dimensional (2D) graphyne or graphdiyne networks. However, the realization of the envisioned regular low-dimensional compounds and nanoarchitectures poses formidable challenges when following conventional synthesis protocols in solution, which we briefly overview. Now, recent developments in on-surface synthesis establish novel means for the construction of tailored covalent nanostructures under ultrahigh vacuum conditions. Here we focus on the exploration of pathways utilizing interfacial synthesis with terminal alkynes toward the atomically precise fabrication of low-dimensional carbon-rich scaffolds and nanomaterials. We review direct, molecular-level investigations, mainly relying on scanning probe microscopy, providing atomistic insights into thermally activated reaction schemes, their special pathways and products. Using custom-made molecular units, the employed homocoupling, cyclotrimerization, cycloaddition, and radical cyclization processes indeed yield distinct compounds, extended oligomers or 2D networks. Detailed insights into surface interactions such as bonding sites or conformational adaptation, and specific reaction mechanisms, including hierarchic pathways, were gained by sophisticated density functional theory calculations, complemented by X-ray spectroscopy measurements. For the fabrication of regular nanostructures and architectures, it is moreover imperative to cope with spurious side reactions, frequently resulting in chemical diversity. Accordingly, we highlight measures for increasing chemo- and regioselectivity by smart precursor design, substrate templating, and external stimuli. The ensuing preorganization of functional groups and control of side reactions increases product yields markedly. Finally, the electronic band structures of selected cases of novel low-dimensional hydrocarbon materials accessible with the monomers employed to date are discussed with a specific focus on their differences to theoretically established graphyne- and graphdiyne-related scaffolds. The presented methodology and gained insights herald further advancements in the field, heading toward novel molecular compounds, low-dimensional nanostructures, and coherently reticulated polymeric layers, eventually presenting well-defined arrangements with specific carbon carbon bond sequencing and electronic characteristics. The functional properties of these or other foreseeable scaffolds and architectures bear significant prospects for a wide range of applications, for example, in nanoelectronics, photonics, or carbon-based technologies.

This thesis investigates the structural and electronic properties of graphene, polyaromatic hydrocarbon (PAH) molecules, and other carbon-based materials, when interacting with metallic surfaces, as well as under the influence of different types of perturbations. Density functional theory, incorporating van der Waals interactions, has been employed.

PAH molecules can, with gradual accuracy, be considered as approximations to an infinite graphene layer. A method to estimate the contributions to the binding energies and net charge transfers from different types of carbon atoms and CH groups in graphene- and PAH-metal systems has been generalized. In this extended method, the number and the nature of the functional groups is determined using a first-principles approach, rather than intuitively or through empirical considerations. Relationships between charge transfers, interface dipole moments and work functions in such systems are explored.

Although the electronic structure of physisorbed graphene keeps most of the features of freestanding graphene, the use of large supercells in calculations makes it difficult to resolve the changes introduced in the band structures of such materials. In this thesis, this was the initial motivation for the development of a method to perform the Brillouin zone unfolding of band structures. This method, as initially developed, is shown to be of general use for any periodic structure, and is even further generalized – through the introduction of the unfolding density operator – to tackle the unfolding of the eigenvalues of any arbitrary operator, with both scalar as well as spinor eigenstates.

A combined experimental and theoretical investigation of the self-assembly of a binary mixture of 4,9-diaminoperylene-quinone-3,10-diimine (DPDI) and 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) molecules on Ag(111) is presented. The DFT calculations performed here allow for the investigation of the interplay between molecule-molecule and molecule-surface interactions in the network.

Besides the main results mentioned above, this thesis also incorporates a study of silicon-metal nanostructures, as well as an investigation of the use of hybrid graphene-graphane structures as prototypes for atomically precise design in nanoelectronics.

Abstract [en]

Density functional theory (DFT) calculations were performed in order to investigate the stability and the electronic structure of graphene-gold interfaces. Two configurations were studied: a gold cluster interacting with graphene and different polycyclic aromatic hydrocarbon (PAH) molecules, namely, C6H6 (benzene), C24H12 (coronene), and C54H18 (circumcoronene) adsorbed on an Au(111) surface. Nonlocal interactions were accounted for by using the semiempirical DFT-D2 method of Grimme. A limited set of calculations were also performed by using the first-principles van der Waals density functional method (vdW-DF). Adsorption distances around 3 angstrom and electronic charge transfer values of about (3-13) x 10(-3)e(-) per carbon atom were predicted for all systems. No major changes resulting from the adsorption of the gold cluster were detected in the graphenes density of states. The DFT-D2 results involving the adsorption of the PAH molecules on gold show an estimated binding energy of 73 meV per carbon atom, as well as an electronic charge loss of 0.10 x 10(-2) e(-), also per carbon atom, for an extended graphene sheet adsorbed on a gold surface. The modeling of the adsorption of C6H6 molecule on a gold surface suggests that the vdW-DF method provides more accurate results for the binding energies of such systems, in comparison to pure DFT calculations, which do not take the nonlocal interactions into account, as well as to simulations employing the DFT-D2 method.

Place, publisher, year, edition, pages

American Physical Society, 2012

National Category

Engineering and Technology

Identifiers

Note

Funding Agencies|Swedish Foundation for International Cooperation in Research and Higher Education (STINT)|YR2009-7017|Swedish Research Council (VR)||Available from: 2012-06-08 Created: 2012-06-08 Last updated: 2017-12-07

Abstract [en]

A systematic study of the optical and magnetic excitations of 12 MSi12 and four MSi10 transition metal encapsulating Si cages has been carried out by employing real time time-dependent density functional theory. Criteria for the choice of transition metals (M) are clusters stability, synthesizability, and diversity. It was found that both the optical absorption and the spin-susceptibility spectra are mainly determined by, in decreasing order of importance, (1) the cage shape, (2) the group in the Periodic Table to which M belongs, and (3) the period of M in the Periodic Table. Cages with similar structures and metal species that are close to each other in the Periodic Table possess spectra sharing many similarities; for example, the optical absorption spectra of the MSi12 (M = V, Nb, Ta, Cr, Mo, and W), which are highly symmetric and belong to groups 4 and 5 of the Periodic Table, all share a very distinctive peak at around 4 eV. In all cases, although some of the observed transitions are located at the Si skeleton of the cages, the transition metal species is always significant for the optical absorption and the spin-susceptibility spectra. Our results provide fingerprint data for identification of gas-phase MSi12 and MSi10 by optical absorption spectroscopy.

Abstract [en]

We use a band unfolding technique to recover an effective primitive cell picture of the band structure of graphene under the influence of different types of perturbations. This involves intrinsic perturbations, such as structural defects, and external ones, comprising nitrogen substitutions and the inclusion of graphene in adsorbed systems. In such cases, the band unfolding provides a reliable and efficient tool for quantitatively analyzing the effect of doping and defects on the electronic structure of graphene. We envision that this approach will become a standard method in the computational analysis of graphene's electronic structure in related systems.

Abstract [en]

First-principles calculations demonstrate that line/ribbon defects, resulting from a controlled dehydrogenation in graphane, lead to the formation of low-dimensional electron-rich tracks in a monolayer. The present simulations point out that hybrid graphane-graphene nanostructures exhibit important elements, greatly required for the fabrication of efficient electronic circuits at the atomic level.

Abstract [en]

We perform a theoretical study of the electronic properties of polyaromatic hydrocarbon (PAH) molecules, as well as benzene and graphene, adsorbed on copper and gold. The PAH molecules studied are coronene (C24H12), circumcoronene (C54H18) and circumcircumcoronene (C96H24), which we consider as gradual approximations to an infinite graphene layer. In order to understand how the size of the adsorbed PAH molecules influences the adsorbate-metal interactions, we generalize the approach used in our earlier study [Phys Rev B, 85 (2012), p. 205423] to decompose the binding energies and net charge transfers into separate contributions from specific groups of atoms, and we then show that the zigzag edges of the PAH molecules interact stronger with the metal surfaces than the armchair ones. We discuss the nature of binding in our model systems as well as the formation of interface dipoles. We show that for all model systems studied here, the charge rearrangement contribution to the interface dipoles can be expressed as the product of the charge involved in the formation of the dipole and the distance between well-defined centers of charge for electron accumulation and depletion. This distance is only marginally dependent on the specific PAH molecules, decreasing slowly with their size.

National Category

Identifiers

Note

P. V. C. M, S. S., and J.B. acknowledge the Swedish Research Council (VR) for funding. S. S. T. acknowledges funding from the University of Basque Country UPV/EHU (GIC07-IT-756-13), the Departamento de Educacion del Gobierno Vasco and the Spanish Ministerio de Ciencia e Innovacion (FIS2010-19609-C02-01), the Tomsk State University Competitiveness Improvement Program, the Saint Petersburg State University (project 11.50.202.2015) and the Spanish Ministry of Economy and Competitiveness MINECO (FIS2013-48286-C2-1-P). Computer resources were allocated by the National Supercomputer Centre, Sweden, through SNAC and the MATTER consortium, as well as in the SKIF-Cyberia and CRYSTAL supercomputers at Tomsk State University.

Björk, Jonas

Stöhr, Meike

Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.

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(English)Manuscript (preprint) (Other academic)

Abstract [en]

We present a combined experimental and theoretical investigation of the self-assembly of a binary mixture of 4,9-diaminoperylene-quinone-3,10-diimine (DPDI) and 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) molecules on Ag(111). At a 1:1 ratio, the two molecules intermix to form a long-range ordered bimolecular network stabilized by intermolecular hydrogen bonding. We show, by means of low energy electron diffraction (LEED) measurements, that the self-assembled network is commensurate with the underlying silver surface. Scanning tunneling microscope (STM) measurements and density functional theory (DFT) calculations are combined to unravel the structural configuration of the system. Core-level binding energy shifts for the 1s levels of the O atoms, obtained from both X-ray photoelectron spectroscopy (XPS) measurements and DFT simulations, are reported and compared. Our DFT calculations allow the investigation of the interplay between molecule-molecule and molecule-surface interactions in the network. Our combined experimental-theoretical approach allows a precise characterization of the structural and electronic properties of the studied system.

We present a combined experimental and theoretical investigation of the self-assembly of a binary mixture of 4,9-diaminoperylene-quinone-3,10-diimine (DPDI) and 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) molecules on Ag(111). At a 1:1 ratio, the two molecules intermix to form a long-range ordered bimolecular network stabilized by intermolecular hydrogen bonding. We show, by means of low energy electron diffraction (LEED) measurements, that the self-assembled network is commensurate with the underlying silver surface. Scanning tunneling microscope (STM) measurements and density functional theory (DFT) calculations are combined to unravel the structural configuration of the system. Core-level binding energy shifts for the 1s levels of the O atoms, obtained from both X-ray photoelectron spectroscopy (XPS) measurements and DFT simulations, are reported and compared. Our DFT calculations allow the investigation of the interplay between molecule-molecule and molecule-surface interactions in the network. Our combined experimental-theoretical approach allows a precise characterization of the structural and electronic properties of the studied system.

The first-order hyperpolarizability, beta, has been calculated for a group Of marine natural products, the makaluvamines. These compounds possess a common Cationic pyrroloiminoquinone structure that is substituted to varying degrees. Calculations at the MP2 level indicate that makaluvamines possessing phenolic side Chains conjugated with the pyrroloiminoquinone moiety display large beta values, while breaking this conjugation leads to a dramatic decrease in the calculated hyperpolarizability. This is consistent with a charge-transfer donor-pi-acceptor (D-pi-A) structure type, characteristic of nonlinear optical Chromophores. Dynamic hyperpolarizabilities calculated using resonance-convergent time-dependent density functional theory coupled to polarizable continuum model (PCM) solvation suggest that significant resonance, enhancement, effects can be expected for incident radiation with wavelengths around 800 nm. The results of the current Work suggest that the pyrroloiminoquinone moiety represents a potentially useful new Chromophore subunit, in particular for the development of molecular probes for biological imaging. The introduction of solvent solute interactions in the theory is conventionally made in a density matrix formalism, and the Present work will provide detailed account of the approximations that need to be introduced in wave function theory, and our program implementation. The program implementation as such is achieved by a mere combination of existing modules from previous developments, and it is here only briefly reviewed.

Polymerization of 1,3,5-tris(4-bromophenyl)benzene via dehalogenation on graphene and hexagonal boron nitride is investigated by scanning tunneling microscopy experiments and density functional theory calculations. This work reveals how the interactions between molecules and graphene or h-BN grown on Ni(111) govern the surface-confined synthesis of polymers through C–C coupling.